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One way to do that is to follow our setup instructions (this is important because a .zip download of the source code doesn't contain binary assets, so that results in a broken version): https://github.com/Revolutionary-Games/Thrive/blob/master/doc/setup_instructions.md If you don't want to distribute your changes you might be perfectly happy running the game from the Godot editor with changes you make. Someone did post the game source code along with binary assets on the forums: https://community.revolutionarygamesstudio.com/t/moddable-thrive-files/3690 with those you could get by without installing Git, but basically everything else is still needed from the setup instructions (well not really all if you don't plan to work on translations, or package the game, you can skip quite many required tools).
Another way is to use a special tool https://github.com/hhyyrylainen/GodotPckTool to extract the Thrive.pck file provided with the game, modify the files (note that if you want to modify things like textures you need to use Godot editor to import those resources to the Godot .stex format), and then re-pack the .pck file with that tool. This is cumbersome currently because we don't have proper mod support in the game (any help implementing this is very much welcome): https://github.com/Revolutionary-Games/Thrive/pull/1521